It was, says the man who played Eliot Ness to US Postal's mobsters, his lowest ebb. When Lance Amstrong decided he was not going to fight on, but still refused to confess despite the weight of evidence against him, the United States anti-doping chief executive, Travis Tygart, despaired.

Vilified by Armstrong's expensively assembled PR operation and the legion of fans that still believed in his Livestrong credo, while knowing publication of the document that laid bare the extent of the doping conspiracy that delivered Armstrong's seven Tour de France victories was still some weeks off, Tygart was frustrated not so much at his intransigence in the face of all available evidence but at the scale of the opportunity missed.

"Remember, we gave him an opportunity to come in and be truthful. That was probably the lowest point for me, because I really thought the change for sport and the legacy of this effort could have been huge, far bigger if he had embraced being a solution rather than an ongoing problem," says Tygart, who says it is not too late for Armstrong to change his mind and tell the truth.

"I just know the power of an athlete in that predicament. We had 11 athletes come forward and their stories are what has allowed this to happen and they're very powerful," says Tygart.

"To be the one, with the reach and the appeal he has, could have taken it to a whole new level as far as the good that could come from it is concerned. It would be as big as we've ever seen in terms of promoting the integrity and the values of sport."

That possibility appears remote. Deserted by his sponsors and most of his supporters, Armstrong remains increasingly isolated but seemingly defiant. Despite the longstanding rumours and allegations, the publication in October of Usada's reasons for stripping Armstrong of his seven Tour de France titles sent shockwaves around the world.

"Somebody said the mob left Vegas and it took over US Postal Pro Cycling team. That's how they operate. The evidence supports it. Our notice letter used terms like 'enforcer' and 'omerta' and 'code of silence'. They are powerful and strong and serious words. But the evidence that supports that is serious too. If anything it was an understatement," he says of evidence collated during a lengthy investigation.

The straight-talking Tygart, a former athlete and lawyer before joining Usada in 2002 and becoming chief executive in 2007, has pursued Armstrong and his entourage in the face of extreme pressure. He says the personal attacks – he has been accused of waging a vendetta and much, much worse – go with the territory. "There are PR operatives who are paid a lot of money to set it up like that. Their MO, forever, has been to find whoever the individual is – whether it's a witness coming forward or a federal agent doing their job or whether it's us doing our job – and make it a personal attack," he says. "We've seen it in other high-profile cases. That's why we're here. We want to take that anger, that venom. We're here to take the heat for clean athletes. We should be the safe harbour."

Once the truth about the scale of the Amstrong "grand heist" began to emerge, Tygart said there was no way that Usada could not pursue it. "We heard the evidence. I sat there and heard the stories. I looked Dave Zabriskie in the eye and heard how as a young kid he grew up in an abusive family, his dad sold drugs, and he ran to cycling to escape. Only to find out a few years later he'd been pulled back in to the very thing he was trying to get away from. I knew, and our board knew, we couldn't let that sit idle," he says.

But the attacks have gone further than harsh words on the internet or smears in the press. Since the investigation began, Tygart has been the subject of at least three credible death threats. He says, almost blithely, that they go with the territory too. "You never like it, of course, but we've come to expect it. My uncle is a judge and I remember that growing up as a kid, he would get death threats all the time. I remember he made some joke about it when my predecessor got a death threat, saying that he thought I went into sport to avoid all this kind of stuff," he says. "We now know, since Balco, that it is what it is. What would be terrible would be if it caused us not to fulful our obligation to those who we've sworn an oath to protect."

Tygart was also at Usada during the Balco case, as the US began the tough task of confronting its demons head on and attempting to unpick a doping conspiracy on an industrial scale within its feted track team. He sees many parallels between the two.

"Marion Jones was beloved. She had investigators following us around and attacked my predecessor as chief executive. When high-profile celebrity athletes have led a sporting fraud and get caught, it's a question of how big their following is and their celebrity is."

Usada's relationship with cycling's world governing body has been fractured to say the least. The UCI refused to endorse Usada's decision to strip Armstrong of his titles until several weeks after the full reasoned decision was published. Even after it had done so at a press conference that quickly degenerated into an attempt to defend its own role in the saga, it hit out at the way Usada had pursued Armstrong and the language in its report.

"Actions speak louder than words. They had an opportunity to support us from the beginning and not do a flip-flip and attack us in the press, attack our authority, attack our jurisdiction. Then they had an opportunity to fully embrace the right outcome, which the entire world – including a number of corporate sponsors – embraced and not again justify or look for excuses for their failure," says Tygart forcefully. "It's not about assigning percentages to failure. Anyone who cares about clean athletes, whether you run the sport of cycling, or run an anti-doping agency or are in the media or sports fans, we have collectively failed if we have condoned or failed to stop a culture that is rife with cheating. We should all take responsibility for that and find definitive ways to recognise the problem, fully expose it and find ways to ensure it never happens again.

"The justification that came out seemed to be full of excuses, not solutions going forward. It's very selfish. It's very self-interested, rather than being for a bigger purpose or a bigger vision. It's very defensive."

The Usada report raised significant questions about the UCI's role. It was accused by two witnesses of covering up a positive test for Amstrong and faced further questions over why it accepted two significant donations from Armstrong. It has admitted receiving the payments but strongly denies they were linked to any failed drug tests and, therefore, denies any cover-up. Tygart is still pushing the UCI to hand over documents relating to an alleged failed test during the 2001 Tour of Switzerland.

"We asked for the documents repeatedly and we were turned down, despite an agreement to obtain them, on numerous occasions. We'd still love to see the documents, to exonerate or otherwise. We were told they exist in summer 2010 and we're still waiting for them. It has to be followed up and the commission that has been formed is going to follow up on that."

The independent commission set up by the UCI to examine a series of questions around the Armstrong affair is cautiously welcomed by Tygart but he has reservations, shared by the World Anti-Doping Agency, over whether its remit is broad enough.

"The people are esteemed and well respected. Where we have concerns are the terms of reference, that they are overly narrow and seem to handcuff and blindfold. That's an obvious concern. Even Interpol, with blinders on and handcuffs on and a straitjacket is not going to do anything," says Tygart.

"The people are great. There are the obvious questions of their independence and then you look at their narrow terms of reference and there are a lot of questions there that need to be answered."

Many question whether the UCI president, Pat McQuaid, and his predecessor, Hein Verbruggen, who is still honorary president, can remain in post after all that has happened. "The answers need to be determined. How in the world does this happen on someone's watch and that person not feel any sense of responsibility about it? That's an obvious question that should be pursued. But it's not really for us to say," says Tygart.

McQuaid defended himself and Verbruggen when announcing that the UCI accepted Usada's decision on Armstrong, saying that he and his predecessor had done all they could to fight doping and the solution now was to look to the future.

Many in cycling have argued that it is being singled out unfairly and that other sports have just as deep rooted doping problems that they have yet to confront. Tygart has little truck with the argument.

"I've heard that and I've heard UCI say it quite a bit and it's just excuses. It's time for bold action for a clean sport. There might be some short-term negative publicity but it will be for the long-term sustainability of the sport. There is no logic reason not to do it."

And he is just as dismissive of the "they were all at it" justification. "If it's a justification that it's OK, they're pros, they all do it anyway – then the question becomes, for mums and dads out there, at what age are you willing to inject a steroid or other performance-enhancing drug into your child because that's what it takes to get to the next level. Eventually, that next level is going to be the 10-year-old soccer team, the junior high team."

Against the backdrop of Wada's ongoing code review, which recommends strengthening the penalty for serious doping offences to four years, Tygart wants to ensure better co-operation between anti-doping agencies and law enforcement on a global basis and to ensure that there is enough investment in both testing and intelligence-led policing. Wada, engaged in a constant arms race to try to keep up with the cheats, continually warn that too few blood tests are being carried out globally for EPO and human growth hormone.

"I think it's about investment. The research we've done in the US clearly shows the threat of performance-enhancing drugs in sport is one of the main issues that Americans are most concerned about, in addition to the criminal behaviour of celebrity role-model athletes," says Tygart, as we struggle to talk over the tinkling of a piano in the incongruous surroundings of a hotel lobby in Doha, where he has been invited to speak at a conference. "You look at the total dollars going into sport and it's a miniscule amount going into anti-doping. This is not easy work. It's tough work, it's complex work. It's a resource issue. We need to do more testing around the world. Several speakers here, from President Sarkozy to Sepp Blatter to the Emir, they referred to sport as the universal religion. Well, if we're talking about the rules of the world's religion then we have to invest to ensure everyone is playing by the rules."

For all that, Tygart is optimistic that the Armstrong case will come to be seen as a watershed in the battle with cheats, proving that a "win at all costs" mentality does have consequences. "We hope it will be a watershed moment for sport, not just cycling. The issues we uncovered transcend sport. They go to the heart of universal principles in every industry. We hope that 10 years from now people will look back on this as being for the good of the values we all want to practise."